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For: Fischer D, Lin SL, Wolfson HL, Nussinov R. A geometry-based suite of molecular docking processes. J Mol Biol 1995;248:459-77. [PMID: 7739053 DOI: 10.1016/s0022-2836(95)80063-8] [Citation(s) in RCA: 87] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Number Cited by Other Article(s)
1
Zhang Y, Wang X, Zhang Z, Huang Y, Kihara D. Assessment of Protein-Protein Docking Models Using Deep Learning. Methods Mol Biol 2024;2780:149-162. [PMID: 38987469 DOI: 10.1007/978-1-0716-3985-6_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2024]
2
Jarończyk M, Abagyan R, Totrov M. Software and Databases for Protein-Protein Docking. Methods Mol Biol 2024;2780:129-138. [PMID: 38987467 DOI: 10.1007/978-1-0716-3985-6_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2024]
3
Chen Z, Liu N, Huang Y, Min X, Zeng X, Ge S, Zhang J, Xia N. PointDE: Protein Docking Evaluation Using 3D Point Cloud Neural Network. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023;20:3128-3138. [PMID: 37220029 DOI: 10.1109/tcbb.2023.3279019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
4
Fenanir F, Semmeq A, Benguerba Y, Badawi M, Dziurla MA, Amira S, Laouer H. In silico investigations of some Cyperus rotundus compounds as potential anti-inflammatory inhibitors of 5-LO and LTA4H enzymes. J Biomol Struct Dyn 2022;40:11571-11586. [PMID: 34355673 DOI: 10.1080/07391102.2021.1960197] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
5
Protein-Protein Docking: Past, Present, and Future. Protein J 2021;41:1-26. [PMID: 34787783 DOI: 10.1007/s10930-021-10031-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/01/2021] [Indexed: 10/19/2022]
6
Wang X, Flannery ST, Kihara D. Protein Docking Model Evaluation by Graph Neural Networks. Front Mol Biosci 2021;8:647915. [PMID: 34113650 PMCID: PMC8185212 DOI: 10.3389/fmolb.2021.647915] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 04/26/2021] [Indexed: 12/03/2022]  Open
7
Slater O, Miller B, Kontoyianni M. Decoding Protein-protein Interactions: An Overview. Curr Top Med Chem 2021;20:855-882. [PMID: 32101126 DOI: 10.2174/1568026620666200226105312] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Revised: 11/27/2019] [Accepted: 11/27/2019] [Indexed: 12/24/2022]
8
Wang X, Terashi G, Christoffer CW, Zhu M, Kihara D. Protein docking model evaluation by 3D deep convolutional neural networks. Bioinformatics 2020;36:2113-2118. [PMID: 31746961 DOI: 10.1093/bioinformatics/btz870] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 08/25/2019] [Accepted: 11/19/2019] [Indexed: 02/06/2023]  Open
9
Pushing the accuracy limit of shape complementarity for protein-protein docking. BMC Bioinformatics 2019;20:696. [PMID: 31874620 PMCID: PMC6929408 DOI: 10.1186/s12859-019-3270-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]  Open
10
Inbar Y, Wolfson HJ, Nussinov R. Multiple Docking for Protein Structure Prediction. Int J Rob Res 2016. [DOI: 10.1177/0278364905050358] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
11
Maheshwari S, Brylinski M. Predicted binding site information improves model ranking in protein docking using experimental and computer-generated target structures. BMC STRUCTURAL BIOLOGY 2015;15:23. [PMID: 26597230 PMCID: PMC4657198 DOI: 10.1186/s12900-015-0050-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 10/30/2015] [Indexed: 01/10/2023]
12
Hashmi I, Shehu A. idDock+: Integrating Machine Learning in Probabilistic Search for Protein–Protein Docking. J Comput Biol 2015. [DOI: 10.1089/cmb.2015.0108] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]  Open
13
Janin J, Wodak SJ, Lensink MF, Velankar S. Assessing Structural Predictions of Protein-Protein Recognition: The CAPRI Experiment. REVIEWS IN COMPUTATIONAL CHEMISTRY 2015. [DOI: 10.1002/9781118889886.ch4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
14
Parikh HI, Kellogg GE. Intuitive, but not simple: including explicit water molecules in protein-protein docking simulations improves model quality. Proteins 2013;82:916-32. [PMID: 24214407 DOI: 10.1002/prot.24466] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Revised: 10/18/2013] [Accepted: 10/22/2013] [Indexed: 11/06/2022]
15
Hashmi I, Shehu A. HopDock: a probabilistic search algorithm for decoy sampling in protein-protein docking. Proteome Sci 2013;11:S6. [PMID: 24564839 PMCID: PMC3909090 DOI: 10.1186/1477-5956-11-s1-s6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]  Open
16
Murakami Y, Kinoshita K, Kinjo AR, Nakamura H. Exhaustive comparison and classification of ligand-binding surfaces in proteins. Protein Sci 2013;22:1379-91. [PMID: 23934772 PMCID: PMC3795496 DOI: 10.1002/pro.2329] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Revised: 07/29/2013] [Accepted: 08/05/2013] [Indexed: 12/03/2022]
17
Wright JD, Sargsyan K, Wu X, Brooks BR, Lim C. Protein-Protein Docking Using EMAP in CHARMM and Support Vector Machine: Application to Ab/Ag Complexes. J Chem Theory Comput 2013;9:4186-94. [PMID: 26592408 DOI: 10.1021/ct400508s] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
18
Axenopoulos A, Daras P, Papadopoulos GE, Houstis EN. SP-dock: protein-protein docking using shape and physicochemical complementarity. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2013;10:135-150. [PMID: 23702550 DOI: 10.1109/tcbb.2012.149] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
19
Wu MY, Dai DQ, Yan H. PRL-dock: Protein-ligand docking based on hydrogen bond matching and probabilistic relaxation labeling. Proteins 2012;80:2137-53. [DOI: 10.1002/prot.24104] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Revised: 04/14/2012] [Accepted: 04/17/2012] [Indexed: 11/08/2022]
20
Li B, Kihara D. Protein docking prediction using predicted protein-protein interface. BMC Bioinformatics 2012;13:7. [PMID: 22233443 PMCID: PMC3287255 DOI: 10.1186/1471-2105-13-7] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2011] [Accepted: 01/10/2012] [Indexed: 11/10/2022]  Open
21
Axenopoulos A, Daras P, Papadopoulos G, Houstis EN. A shape descriptor for fast complementarity matching in molecular docking. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2011;8:1441-1457. [PMID: 21519110 DOI: 10.1109/tcbb.2011.72] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
22
Mitra P, Pal D. PRUNE and PROBE--two modular web services for protein-protein docking. Nucleic Acids Res 2011;39:W229-34. [PMID: 21576226 PMCID: PMC3125751 DOI: 10.1093/nar/gkr317] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
23
Bajaj C, Chowdhury R, Siddavanahalli V. F2Dock: fast Fourier protein-protein docking. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2011;8:45-58. [PMID: 21071796 PMCID: PMC3058388 DOI: 10.1109/tcbb.2009.57] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
24
Solernou A, Fernandez-Recio J. Protein docking by Rotation-Based Uniform Sampling (RotBUS) with fast computing of intermolecular contact distance and residue desolvation. BMC Bioinformatics 2010;11:352. [PMID: 20584304 PMCID: PMC2911459 DOI: 10.1186/1471-2105-11-352] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2009] [Accepted: 06/28/2010] [Indexed: 11/27/2022]  Open
25
Molecular surface mesh generation by filtering electron density map. Int J Biomed Imaging 2010;2010:923780. [PMID: 20414352 PMCID: PMC2856016 DOI: 10.1155/2010/923780] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2009] [Revised: 11/23/2009] [Accepted: 01/06/2010] [Indexed: 11/17/2022]  Open
26
Chae MH, Krull F, Lorenzen S, Knapp EW. Predicting protein complex geometries with a neural network. Proteins 2010;78:1026-39. [PMID: 19938153 DOI: 10.1002/prot.22626] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
27
Ravikant DVS, Elber R. PIE-efficient filters and coarse grained potentials for unbound protein-protein docking. Proteins 2010;78:400-19. [PMID: 19768784 DOI: 10.1002/prot.22550] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
28
Venkatraman V, Yang YD, Sael L, Kihara D. Protein-protein docking using region-based 3D Zernike descriptors. BMC Bioinformatics 2009;10:407. [PMID: 20003235 PMCID: PMC2800122 DOI: 10.1186/1471-2105-10-407] [Citation(s) in RCA: 126] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2009] [Accepted: 12/09/2009] [Indexed: 12/02/2022]  Open
29
Zhang Q, Sanner M, Olson AJ. Shape complementarity of protein-protein complexes at multiple resolutions. Proteins 2009;75:453-67. [PMID: 18837463 PMCID: PMC2928789 DOI: 10.1002/prot.22256] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
30
Del Carpio CA, Iulian Florea M, Suzuki A, Tsuboi H, Hatakeyama N, Endou A, Takaba H, Ichiishi E, Miyamoto A. A graph theoretical approach for assessing bio-macromolecular complex structural stability. J Mol Model 2009;15:1349-70. [PMID: 19408019 DOI: 10.1007/s00894-009-0494-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2008] [Accepted: 02/25/2009] [Indexed: 11/24/2022]
31
Andrusier N, Mashiach E, Nussinov R, Wolfson HJ. Principles of flexible protein-protein docking. Proteins 2009;73:271-89. [PMID: 18655061 DOI: 10.1002/prot.22170] [Citation(s) in RCA: 159] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
32
A graph theoretical approach to the effect of mutation on the flexibility of the DNA binding domain of p53 protein. CHEMICAL PAPERS 2009. [DOI: 10.2478/s11696-009-0068-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
33
Shen Y, Paschalidis IC, Vakili P, Vajda S. Protein docking by the underestimation of free energy funnels in the space of encounter complexes. PLoS Comput Biol 2008;4:e1000191. [PMID: 18846200 PMCID: PMC2538569 DOI: 10.1371/journal.pcbi.1000191] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2008] [Accepted: 08/22/2008] [Indexed: 11/19/2022]  Open
34
Huang SY, Zou X. An iterative knowledge-based scoring function for protein-protein recognition. Proteins 2008;72:557-79. [PMID: 18247354 DOI: 10.1002/prot.21949] [Citation(s) in RCA: 222] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
35
Shentu Z, Al Hasan M, Bystroff C, Zaki MJ. Context shapes: Efficient complementary shape matching for protein-protein docking. Proteins 2008;70:1056-73. [PMID: 17847098 DOI: 10.1002/prot.21600] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
36
Stahl M. Structure‐Based Library Design. ACTA ACUST UNITED AC 2008. [DOI: 10.1002/9783527613083.ch11] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
37
Andrusier N, Nussinov R, Wolfson HJ. FireDock: fast interaction refinement in molecular docking. Proteins 2007;69:139-59. [PMID: 17598144 DOI: 10.1002/prot.21495] [Citation(s) in RCA: 503] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
38
Bordner AJ, Gorin AA. Protein docking using surface matching and supervised machine learning. Proteins 2007;68:488-502. [PMID: 17444516 DOI: 10.1002/prot.21406] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
39
Pierce B, Weng Z. ZRANK: reranking protein docking predictions with an optimized energy function. Proteins 2007;67:1078-86. [PMID: 17373710 DOI: 10.1002/prot.21373] [Citation(s) in RCA: 354] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
40
Seeliger D, de Groot BL. Atomic contacts in protein structures. A detailed analysis of atomic radii, packing, and overlaps. Proteins 2007;68:595-601. [PMID: 17510956 DOI: 10.1002/prot.21447] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
41
Kuhn D, Weskamp N, Schmitt S, Hüllermeier E, Klebe G. From the similarity analysis of protein cavities to the functional classification of protein families using cavbase. J Mol Biol 2006;359:1023-44. [PMID: 16697007 PMCID: PMC7094329 DOI: 10.1016/j.jmb.2006.04.024] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2006] [Revised: 03/31/2006] [Accepted: 04/06/2006] [Indexed: 02/05/2023]
42
Schneidman-Duhovny D, Inbar Y, Nussinov R, Wolfson HJ. Geometry-based flexible and symmetric protein docking. Proteins 2006;60:224-31. [PMID: 15981269 DOI: 10.1002/prot.20562] [Citation(s) in RCA: 155] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
43
Fischer TB, Holmes JB, Miller IR, Parsons JR, Tung L, Hu JC, Tsai J. Assessing methods for identifying pair-wise atomic contacts across binding interfaces. J Struct Biol 2006;153:103-12. [PMID: 16377205 DOI: 10.1016/j.jsb.2005.11.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2005] [Revised: 09/23/2005] [Accepted: 11/08/2005] [Indexed: 11/29/2022]
44
Schneidman-Duhovny D, Inbar Y, Nussinov R, Wolfson HJ. PatchDock and SymmDock: servers for rigid and symmetric docking. Nucleic Acids Res 2005;33:W363-7. [PMID: 15980490 PMCID: PMC1160241 DOI: 10.1093/nar/gki481] [Citation(s) in RCA: 2164] [Impact Index Per Article: 113.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]  Open
45
Inbar Y, Benyamini H, Nussinov R, Wolfson HJ. Prediction of Multimolecular Assemblies by Multiple Docking. J Mol Biol 2005;349:435-47. [PMID: 15890207 DOI: 10.1016/j.jmb.2005.03.039] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2004] [Revised: 02/01/2005] [Accepted: 03/14/2005] [Indexed: 10/25/2022]
46
Shatsky M, Nussinov R, Wolfson HJ. A method for simultaneous alignment of multiple protein structures. Proteins 2004;56:143-56. [PMID: 15162494 DOI: 10.1002/prot.10628] [Citation(s) in RCA: 348] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
47
Zacharias M. Protein-protein docking with a reduced protein model accounting for side-chain flexibility. Protein Sci 2003;12:1271-82. [PMID: 12761398 PMCID: PMC2323887 DOI: 10.1110/ps.0239303] [Citation(s) in RCA: 244] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2002] [Revised: 02/07/2003] [Accepted: 02/28/2003] [Indexed: 10/27/2022]
48
Wodak SJ, Janin J. Structural basis of macromolecular recognition. ADVANCES IN PROTEIN CHEMISTRY 2003;61:9-73. [PMID: 12461820 DOI: 10.1016/s0065-3233(02)61001-0] [Citation(s) in RCA: 119] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
49
Zavodszky MI, Sanschagrin PC, Korde RS, Kuhn LA. Distilling the essential features of a protein surface for improving protein-ligand docking, scoring, and virtual screening. J Comput Aided Mol Des 2002;16:883-902. [PMID: 12825621 DOI: 10.1023/a:1023866311551] [Citation(s) in RCA: 81] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
50
Del Carpio-Muñoz CA, Ichiishi E, Yoshimori A, Yoshikawa T. MIAX: a new paradigm for modeling biomacromolecular interactions and complex formation in condensed phases. Proteins 2002;48:696-732. [PMID: 12211037 DOI: 10.1002/prot.10122] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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